ClinVar Miner

Submissions for variant NM_000051.3(ATM):c.6754del (p.Thr2252fs) (rs1064793042)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000485978 SCV000564653 pathogenic not provided 2015-02-10 criteria provided, single submitter clinical testing This deletion of one nucleotide in ATM is denoted c.6754delA at the cDNA level and p.Thr2252ProfsX5 (T2252PfsX5) at the protein level. The normal sequence, with the base that is deleted in brackets, is TCTC[A]CCAA. The deletion causes a frameshift, which changes a Threonine to a Proline at codon 2252, and creates a premature stop codon at position 5 of the new reading frame. This variant is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. ATM c.6754delA has been reported in the compound heterozygous state with another pathogenic ATM variant in a patient with ataxia telangiectasia (Podralska 2014). we consider this variant to be pathogenic. The presence of
Invitae RCV000816022 SCV000956510 pathogenic Ataxia-telangiectasia syndrome 2018-09-12 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Thr2252Profs*5) in the ATM gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in an individual affected with ataxia-telangiectasia (PMID: 25614872). ClinVar contains an entry for this variant (Variation ID: 418040). Loss-of-function variants in ATM are known to be pathogenic (PMID: 23807571, 25614872). For these reasons, this variant has been classified as Pathogenic.

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